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- PDB-6pq1: Structure of the Fremyella diplosiphon OCP1 -

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Basic information

Entry
Database: PDB / ID: 6pq1
TitleStructure of the Fremyella diplosiphon OCP1
ComponentsOrange carotenoid-binding protein
KeywordsPHOTOSYNTHESIS / PHOTOPROTECTION / CAROTENOID BINDING PROTEIN
Function / homology
Function and homology information


light absorption / : / phycobilisome / chloride ion binding
Similarity search - Function
orange carotenoid protein, domain 2 / Orange carotenoid-binding protein, N-terminal domain / Orange carotenoid-binding protein, N-terminal / Orange carotenoid-binding protein, N-terminal domain superfamily / Orange carotenoid protein, N-terminal / Orange carotenoid protein (OCP) N-terminal domain profile. / Nuclear transport factor 2 domain / Nuclear transport factor 2 (NTF2) domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily ...orange carotenoid protein, domain 2 / Orange carotenoid-binding protein, N-terminal domain / Orange carotenoid-binding protein, N-terminal / Orange carotenoid-binding protein, N-terminal domain superfamily / Orange carotenoid protein, N-terminal / Orange carotenoid protein (OCP) N-terminal domain profile. / Nuclear transport factor 2 domain / Nuclear transport factor 2 (NTF2) domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
beta,beta-carotene-4,4'-dione / Orange carotenoid-binding protein
Similarity search - Component
Biological speciesTolypothrix sp. PCC 7601 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsSutter, M. / Dominguez-Martin, M.A. / Bao, H. / Kerfeld, C.A.
CitationJournal: Biochim Biophys Acta Bioenerg / Year: 2020
Title: Comparative ultrafast spectroscopy and structural analysis of OCP1 and OCP2 from Tolypothrix.
Authors: Kuznetsova, V. / Dominguez-Martin, M.A. / Bao, H. / Gupta, S. / Sutter, M. / Kloz, M. / Rebarz, M. / Precek, M. / Chen, Y. / Petzold, C.J. / Ralston, C.Y. / Kerfeld, C.A. / Polivka, T.
History
DepositionJul 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Orange carotenoid-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0142
Polymers36,4501
Non-polymers5651
Water4,576254
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.019, 95.019, 78.523
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z

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Components

#1: Protein Orange carotenoid-binding protein


Mass: 36449.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tolypothrix sp. PCC 7601 (bacteria) / Gene: FDUTEX481_08602 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0D6KM24
#2: Chemical ChemComp-45D / beta,beta-carotene-4,4'-dione / Isomer of Canthaxanthin


Mass: 564.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C40H52O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57.18 %
Crystal growTemperature: 277 K / Method: batch mode / pH: 7 / Details: 0.75 M potassium phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.61→41.14 Å / Num. obs: 51011 / % possible obs: 96 % / Redundancy: 9.5 % / Biso Wilson estimate: 25.7 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.037 / Net I/σ(I): 27.9
Reflection shellResolution: 1.61→1.7 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.385 / Mean I/σ(I) obs: 5 / Num. unique obs: 7600 / CC1/2: 0.953 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MG1

3mg1


Resolution: 1.61→41.14 Å / SU ML: 0.1711 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.298
RfactorNum. reflection% reflectionSelection details
Rfree0.2128 1987 3.92 %Random selection
Rwork0.1948 ---
obs0.1956 50661 95.41 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 34.62 Å2
Refinement stepCycle: LAST / Resolution: 1.61→41.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2506 0 42 254 2802
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01842618
X-RAY DIFFRACTIONf_angle_d1.56893571
X-RAY DIFFRACTIONf_chiral_restr0.0889397
X-RAY DIFFRACTIONf_plane_restr0.0132468
X-RAY DIFFRACTIONf_dihedral_angle_d11.5832174
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.61-1.650.30071410.25163501X-RAY DIFFRACTION98.54
1.65-1.70.28111530.23213653X-RAY DIFFRACTION100
1.7-1.750.26051440.22813579X-RAY DIFFRACTION99.95
1.75-1.80.24871450.22943613X-RAY DIFFRACTION100
1.8-1.870.24221500.23613635X-RAY DIFFRACTION99.89
1.87-1.940.36441320.30473353X-RAY DIFFRACTION93.48
1.94-2.030.28461470.23233620X-RAY DIFFRACTION99.58
2.03-2.140.24151480.21633618X-RAY DIFFRACTION99.89
2.14-2.270.2361160.21922752X-RAY DIFFRACTION98.05
2.27-2.450.22721260.19443035X-RAY DIFFRACTION99.34
2.45-2.690.19461450.20083647X-RAY DIFFRACTION99.82
2.69-3.080.24151510.19553674X-RAY DIFFRACTION99.95
3.08-3.880.21731330.18353163X-RAY DIFFRACTION85.7
3.88-41.140.14751560.15723831X-RAY DIFFRACTION99.97

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